This is a really interesting point.
We know for a fact that Hermione has been manipulated because we've seen the scene with Hat and Cloak. That may bias us in favor of thinking the evidence is clearer than it really is. Yet Harry knows that in this universe memories can be tampered with. The prior probability of a morally upstanding little girl trying to murder someone is much less than the prior probability of someone else trying the memory-charm plot, especially given that Hermione is friends with Harry and Harry's status as the Boy Who Lived makes him a target.
Now, I might put a probability of something like 0.2 on the possibility of Hermione casting the charm after someone messed with her mind. But if you're the plotter, it's so much easier to do a false memory charm to make her remember casting the charm, than to do all the delicate manipulation to get her to actually cast it. So more likely than not, Hermione didn't cast the charm.
Harry is making a subtle mistake here, though: he's over-confident about his ideas about the details of what was done to Hermione. For example, he thinks a false-memory charm was used to cause Hermione to start obsessing over Draco, when in fact that was based on true memories of a conversation (albeit one involving lies and some kind of shape-shifting/illusion magic). Feminist bank tellers and all that.
On the last point: Hermione almost certainly was false memory charmed twice; H&C would have removed the memory of their final conversation and replaced with with something innocuous at the same time as he implanted the false memory of casting the blood-cooling charm, so as to not leave a suspicious gap. He might also have implanted false memories immediately after the groundhog day attack, either to cover up the time gap or to not have Hermione wandering around with an extremely suspicious memory in her head (If Dumbledore or Snape had seen the memory of H&C, or his less-creepy disguise, they probably would have been fairly suspicious).
The new discussion thread (part 15) is here.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 82. The previous thread passed 1000 comments as of the time of this writing, and so has long passed 500. Comment in the 13th thread until you read chapter 82.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13.
As a reminder, it’s often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: